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<!-- doxytag: class="moltk::MatrixScorer" --><!-- doxytag: inherits="moltk::Aligner::Scorer" -->
<p><a class="el" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a> scores alignments using a residue type matrix such as BLOSUM62 or PAM250.  
 <a href="classmoltk_1_1MatrixScorer.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="MatrixScorer_8hpp_source.html">MatrixScorer.hpp</a>&gt;</code></p>
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Inheritance diagram for moltk::MatrixScorer:</div>
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<div class="center"><img src="classmoltk_1_1MatrixScorer__inherit__graph.png" border="0" usemap="#moltk_1_1MatrixScorer_inherit__map" alt="Inheritance graph"/></div>
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<area shape="rect" id="node2" href="classmoltk_1_1Aligner_1_1Scorer.html" title="Scorer can convert, in O(m+n) time, dumb sequence and structure residues into TargetPositions and Que..." alt="" coords="5,5,152,32"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
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Collaboration diagram for moltk::MatrixScorer:</div>
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<area shape="rect" id="node2" href="classmoltk_1_1Aligner_1_1Scorer.html" title="Scorer can convert, in O(m+n) time, dumb sequence and structure residues into TargetPositions and Que..." alt="" coords="605,21,753,48"/><area shape="rect" id="node4" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;." alt="" coords="128,21,325,48"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1MatrixScorer-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html">QueryPosition</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html" title="QueryPosition represents an alignment/sequence column in the second of two sequences being scored by ...">QueryPosition</a> represents an alignment/sequence column in the second of two sequences being scored by a <a class="el" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a>.  <a href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html">TargetPosition</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html" title="TargetPosition represents an alignment/sequence column in the first of two sequences being scored by ...">TargetPosition</a> represents an alignment/sequence column in the first of two sequences being scored by a <a class="el" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a>.  <a href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="namespacemoltk_1_1units.html#a84d2541f1ab08c8ae38bea32fa7b33ca">moltk::units::Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#ab2547e83ca5136945352ab5ef008de4b">Information</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#a679c59d57d0d690fc2add4204b15deb6">MatrixScorer</a> (const std::string &amp;matrix_string)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#adad6226f36c265d3f8f6c204dea3bf72">MatrixScorer</a> (std::istream &amp;matrix_stream)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector<br class="typebreak"/>
&lt; <a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html">Aligner::QueryPosition</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#a6732a8098d7e4811669934618d5ea1ef">create_query_positions</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;alignment) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector<br class="typebreak"/>
&lt; <a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html">Aligner::TargetPosition</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#adadccdab70f7531e88e619a75dcf58c7">create_target_positions</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;alignment) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::istream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#a24d6950d643f55e6613755404c0c305b">load_stream</a> (std::istream &amp;)</td></tr>
<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classmoltk_1_1MatrixScorer.html">MatrixScorer</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#a58a29032f0c197845d1c1cabb4bf2d84">get_blosum62_scorer</a> ()</td></tr>
<tr><td colspan="2"><h2><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr><td class="memTemplParams" colspan="2">template&lt;class POSB , class POS &gt; </td></tr>
<tr><td class="memTemplItemLeft" align="right" valign="top">std::vector&lt; POSB * &gt;&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#aef587746f1419b9b985ee68ff1455f04">create_foo_positions</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;alignment) const </td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; int &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#a6a1606c15fde892eedd8bcd83d2b4350">character_indices</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::vector<br class="typebreak"/>
&lt; <a class="el" href="classmoltk_1_1MatrixScorer.html#ab2547e83ca5136945352ab5ef008de4b">Information</a> &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer.html#ac6fdcde81452d3f0c853b09d0c07f4a9">matrix</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p><a class="el" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a> scores alignments using a residue type matrix such as BLOSUM62 or PAM250. </p>
</div><hr/><h2>Member Typedef Documentation</h2>
<a class="anchor" id="ab2547e83ca5136945352ab5ef008de4b"></a><!-- doxytag: member="moltk::MatrixScorer::Information" ref="ab2547e83ca5136945352ab5ef008de4b" args="" -->
<div class="memitem">
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        <tr>
          <td class="memname">typedef <a class="el" href="namespacemoltk_1_1units.html#a84d2541f1ab08c8ae38bea32fa7b33ca">moltk::units::Information</a> <a class="el" href="classmoltk_1_1MatrixScorer.html#ab2547e83ca5136945352ab5ef008de4b">moltk::MatrixScorer::Information</a></td>
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</div>
<div class="memdoc">

</div>
</div>
<hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="a679c59d57d0d690fc2add4204b15deb6"></a><!-- doxytag: member="moltk::MatrixScorer::MatrixScorer" ref="a679c59d57d0d690fc2add4204b15deb6" args="(const std::string &amp;matrix_string)" -->
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      <table class="memname">
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          <td class="memname">moltk::MatrixScorer::MatrixScorer </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>matrix_string</em></td><td>)</td>
          <td><code> [explicit]</code></td>
        </tr>
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<div class="memdoc">

</div>
</div>
<a class="anchor" id="adad6226f36c265d3f8f6c204dea3bf72"></a><!-- doxytag: member="moltk::MatrixScorer::MatrixScorer" ref="adad6226f36c265d3f8f6c204dea3bf72" args="(std::istream &amp;matrix_stream)" -->
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          <td class="memname">moltk::MatrixScorer::MatrixScorer </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"><em>matrix_stream</em></td><td>)</td>
          <td><code> [explicit]</code></td>
        </tr>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="aef587746f1419b9b985ee68ff1455f04"></a><!-- doxytag: member="moltk::MatrixScorer::create_foo_positions" ref="aef587746f1419b9b985ee68ff1455f04" args="(const Alignment &amp;alignment) const " -->
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<div class="memproto">
<div class="memtemplate">
template&lt;class POSB , class POS &gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">std::vector&lt;POSB*&gt; moltk::MatrixScorer::create_foo_positions </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
          <td class="paramname"><em>alignment</em></td><td>)</td>
          <td> const<code> [protected]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a6732a8098d7e4811669934618d5ea1ef"></a><!-- doxytag: member="moltk::MatrixScorer::create_query_positions" ref="a6732a8098d7e4811669934618d5ea1ef" args="(const Alignment &amp;alignment) const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::vector&lt;<a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html">Aligner::QueryPosition</a>*&gt; moltk::MatrixScorer::create_query_positions </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
          <td class="paramname"><em>alignment</em></td><td>)</td>
          <td> const<code> [virtual]</code></td>
        </tr>
      </table>
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<div class="memdoc">

<p>Implements <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a090273ed5beeae79b7058f647a863d84">moltk::Aligner::Scorer</a>.</p>

</div>
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<a class="anchor" id="adadccdab70f7531e88e619a75dcf58c7"></a><!-- doxytag: member="moltk::MatrixScorer::create_target_positions" ref="adadccdab70f7531e88e619a75dcf58c7" args="(const Alignment &amp;alignment) const " -->
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      <table class="memname">
        <tr>
          <td class="memname">std::vector&lt;<a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html">Aligner::TargetPosition</a>*&gt; moltk::MatrixScorer::create_target_positions </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
          <td class="paramname"><em>alignment</em></td><td>)</td>
          <td> const<code> [virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implements <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#ac699ce5b5c5eb5d06d7875ae3bc6e881">moltk::Aligner::Scorer</a>.</p>

</div>
</div>
<a class="anchor" id="a58a29032f0c197845d1c1cabb4bf2d84"></a><!-- doxytag: member="moltk::MatrixScorer::get_blosum62_scorer" ref="a58a29032f0c197845d1c1cabb4bf2d84" args="()" -->
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      <table class="memname">
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          <td class="memname">static const <a class="el" href="classmoltk_1_1MatrixScorer.html">MatrixScorer</a>&amp; moltk::MatrixScorer::get_blosum62_scorer </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [static]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a24d6950d643f55e6613755404c0c305b"></a><!-- doxytag: member="moltk::MatrixScorer::load_stream" ref="a24d6950d643f55e6613755404c0c305b" args="(std::istream &amp;)" -->
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      <table class="memname">
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          <td class="memname">std::istream&amp; moltk::MatrixScorer::load_stream </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"></td><td>)</td>
          <td></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a6a1606c15fde892eedd8bcd83d2b4350"></a><!-- doxytag: member="moltk::MatrixScorer::character_indices" ref="a6a1606c15fde892eedd8bcd83d2b4350" args="" -->
<div class="memitem">
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      <table class="memname">
        <tr>
          <td class="memname">std::vector&lt;int&gt; <a class="el" href="classmoltk_1_1MatrixScorer.html#a6a1606c15fde892eedd8bcd83d2b4350">moltk::MatrixScorer::character_indices</a><code> [protected]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="ac6fdcde81452d3f0c853b09d0c07f4a9"></a><!-- doxytag: member="moltk::MatrixScorer::matrix" ref="ac6fdcde81452d3f0c853b09d0c07f4a9" args="" -->
<div class="memitem">
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      <table class="memname">
        <tr>
          <td class="memname">std::vector&lt; std::vector&lt;<a class="el" href="classmoltk_1_1MatrixScorer.html#ab2547e83ca5136945352ab5ef008de4b">Information</a>&gt; &gt; <a class="el" href="classmoltk_1_1MatrixScorer.html#ac6fdcde81452d3f0c853b09d0c07f4a9">moltk::MatrixScorer::matrix</a><code> [protected]</code></td>
        </tr>
      </table>
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<div class="memdoc">

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</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="MatrixScorer_8hpp_source.html">MatrixScorer.hpp</a></li>
</ul>
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